def create_hub(geo, email=None, upload=False, upload_dir=".", user=None, host=None):
""" Create an UCSC track hub from a Geo object
"""
hub = Hub(
hub=geo.gse,
short_label=geo.gse,
long_label="Hub for {0}".format(geo.gse),
email=email)
genomes_file = GenomesFile()
trackdb = TrackDb()
local_dir = geo.gse
#hub.remote_fn = os.path.join(upload_dir, geo.gse, os.path.basename(hub.local_fn))
all_tracks = {}
for sample in geo.samples.values():
genome = sample['genome']
all_tracks.setdefault(genome, [])
name = re.sub('[^0-9a-zA-Z]+', '_',sample['name'])
track = Track(
name=name,
url=os.path.join(HUB_URLBASE, geo.gse, genome, "{0}.bw".format(sample['gsm'])),
tracktype='bigWig',
short_label=sample['gsm'],
long_label=name,
color='128,128,0',
maxHeightPixels='30:30:11',
)
basename = os.path.basename(track.url)
track.local_fn = os.path.join(local_dir, basename)
track.remote_fn = os.path.join(upload_dir, geo.gse, genome, basename)
all_tracks[genome].append(track)
for build,tracks in all_tracks.items():
genome = Genome(build)
trackdb.add_tracks(tracks)
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results = hub.render()
if upload:
for track in trackdb.tracks:
upload_track(track=track, host=host, user=user)
upload_hub(hub=hub, host=host, user=user)
class TestUpload(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bam',
local_fn='data/track1.bam'
),
Track(
name='track2',
tracktype='bigWig',
local_fn='data/track2.bigwig',
),
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
@unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data')
def test_upload(self):
self.hub.remote_fn = os.path.join(
'uploaded_version',
self.hub.remote_fn)
self.hub.render()
upload.upload_hub(
'localhost',
None,
self.hub,
symlink=True,
symlink_dir='staging',
run_local=True,)
for t, level in self.hub.leaves(Track):
upload.upload_track(
track=t, host='localhost', user=None, run_local=True)
def test_render(self):
trackdb = str(self.trackdb)
# make sure some of the trackdb rendered correctly
assert 'track track1' in trackdb
assert 'bigDataUrl track1.bam' in trackdb
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bam',
local_fn='data/track1.bam'
),
Track(
name='track2',
tracktype='bigWig',
local_fn='data/track2.bigwig',
),
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bigBed',
source=os.path.join(d, 'random-hg38-0.bigBed')
),
Track(
name='track2',
tracktype='bigWig',
source=os.path.join(d, 'sine-hg38-0.bedgraph.bw'),
),
Track(
name='track3',
tracktype='bigWig',
source=os.path.join(d, 'sine-hg38-1.bedgraph.bw'),
filename='3.bw',
)
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
class TestUpload(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bam',
local_fn='data/track1.bam'
),
Track(
name='track2',
tracktype='bigWig',
local_fn='data/track2.bigwig',
),
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def test_upload(self):
self.hub.remote_fn = os.path.join(
'uploaded_version',
self.hub.remote_fn)
self.hub.render()
upload.upload_hub(
'localhost',
None,
self.hub,
symlink=True,
symlink_dir='staging',
run_local=True,)
for t, level in self.hub.leaves(Track):
upload.upload_track(
track=t, host='localhost', user=None, run_local=True)
def setup(self):
self.hub = Hub(
hub="example_hub",
short_label="example hub",
long_label="an example hub for testing",
email="*****@*****.**",
)
self.genomes_file = GenomesFile()
self.genome = Genome("dm3")
self.trackdb = TrackDb()
self.tracks = [Track(name="track1", tracktype="bam"), Track(name="track2", tracktype="bigWig")]
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(name='track1', tracktype='bam'),
Track(name='track2', tracktype='bigWig'),
]
if not args.long_label:
args.long_label = args.short_label
upload_dir = os.path.join("/zfs/Hubs", args.hub)
URLBASE= os.path.join("http://sauron.ucsd.edu/Hubs", args.hub)
GENOME = args.genome
hub = Hub(hub=args.hub,
short_label=args.short_label,
long_label=args.long_label,
email = args.email,
)
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
hub.upload_fn = upload_dir
files = args.files
#logic for doing pos and neg as the same multi trackhub
#process bw files first, do the rest with old logic
bw_files = [track for track in files if track.endswith(".bw") or track.endswith(".bigWig")]
remaining_files = [track for track in files if not (track.endswith(".bw") or track.endswith(".bigWig"))]
key_func = lambda x: x.split(".")[:-2]
for bw_group, files in groupby(sorted(bw_files, key=key_func), key_func):
long_name = os.path.basename(bw_group[0])
class TestComponents(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(name='track1', tracktype='bam'),
Track(name='track2', tracktype='bigWig'),
]
def CONNECT(self):
"""
Connect the components together. The default setup creates the objects
but does not connect them.
"""
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def DISCONNECT(self):
"""
Re-run the setup, which results in unconnected components. Run
CONNECT() to connect them up.
"""
self.setup()
def test_self_connection(self):
"""
meta test: make sure the test class's connect/disconnect is working
"""
assert self.hub.genomes_file is None
self.CONNECT()
assert self.hub.genomes_file is self.genomes_file
self.DISCONNECT()
assert self.hub.genomes_file is None
# Filenames ---------------------------------------------------------------
def test_hub_fns(self):
# Default unconnected
assert self.hub.filename == 'example_hub.hub.txt'
# Connecting components should not change hub
self.CONNECT()
assert self.hub.filename == 'example_hub.hub.txt'
self.DISCONNECT()
def test_genome_file_fns(self):
with pytest.raises(AttributeError):
getattr(self.genomes_file, 'url')
# When unconnected, filenames should be None
assert self.genomes_file.filename is None
#...though you can set them manually
self.genomes_file.filename = 'local.genomes'
assert self.genomes_file.filename == 'local.genomes'
self.genomes_file.filename = None
self.CONNECT()
assert self.genomes_file.filename == 'example_hub.genomes.txt'
# when connected, overriding works
self.genomes_file.filename = 'local.genomes'
assert self.genomes_file.filename == 'local.genomes'
self.genomes_file.filename = None
# disconnecting brings it back to None
self.DISCONNECT()
assert self.genomes_file.filename is None
# set the hub's local_dir; genomes_file should follow.
self.CONNECT()
# what happens if the hub's local FN is changed?
self.hub.filename = 'localhub/hub.txt'
assert self.genomes_file.filename == 'localhub/example_hub.genomes.txt'
def test_trackdb_fns(self):
# when unconnected, no defaults
assert self.trackdb.filename is None
self.CONNECT()
assert self.trackdb.filename == 'dm3/trackDb.txt'
# setting filename overrides
self.trackdb.filename = 'mytrackdb.txt'
assert self.trackdb.filename == 'mytrackdb.txt', self.trackdb.filename
# genomes_file fn overrides
self.trackdb.filename = None
self.genomes_file.filename = 'anotherdir/genomes.txt'
assert self.trackdb.filename == 'anotherdir/dm3/trackDb.txt'
# reset parent hub and genomes file to get back to the default
self.genomes_file.filename = None
assert self.trackdb.filename == 'dm3/trackDb.txt'
def test_track_fns(self):
self.CONNECT()
# local fns should still be None
for track in self.tracks:
assert track.source is None
# filename is relative to the hub's filename
assert self.tracks[0].filename == 'dm3/track1.bam'
assert self.tracks[1].filename == 'dm3/track2.bigWig'
# URL is relative to the trackDb
assert self.tracks[0].url == 'track1.bam'
def test_track_creation(self):
track = Track(name='track0', tracktype='bam', source='t0.bam')
assert track.source == 't0.bam'
if args.no_s3:
URLBASE = os.path.join("https://s3-us-west-1.amazonaws.com/sauron-yeo/", args.hub)
else:
URLBASE = os.path.join("http://sauron.ucsd.edu/Hubs", args.hub)
GENOME = args.genome
hub = Hub(hub=args.hub,
short_label=args.short_label,
long_label=args.long_label,
email=args.email,
)
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
supertrack = SuperTrack(name=args.hub,
short_label=args.hub,
long_label=args.hub)
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
hub.upload_fn = upload_dir
files = args.files
#logic for doing pos and neg as the same multi trackhub
#process bw files first, do the rest with old logic
bw_files = [track for track in files if
track.endswith(".bw") or track.endswith(".bigWig")]
remaining_files = [track for track in files if
not (track.endswith(".bw") or track.endswith(".bigWig"))]
class TestComponents(object):
def setup(self):
self.hub = Hub(
hub="example_hub",
short_label="example hub",
long_label="an example hub for testing",
email="*****@*****.**",
)
self.genomes_file = GenomesFile()
self.genome = Genome("dm3")
self.trackdb = TrackDb()
self.tracks = [Track(name="track1", tracktype="bam"), Track(name="track2", tracktype="bigWig")]
def CONNECT(self):
"""
Connect the components together. The default setup creates the objects
but does not connect them.
"""
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def DISCONNECT(self):
"""
Re-run the setup, which results in unconnected components. Run
CONNECT() to connect them up.
"""
self.setup()
def test_self_connection(self):
"""
meta test: make sure the test class's connect/disconnect is working
"""
assert self.hub.genomes_file is None
self.CONNECT()
assert self.hub.genomes_file is self.genomes_file
self.DISCONNECT()
assert self.hub.genomes_file is None
# Filenames ---------------------------------------------------------------
def test_hub_fns(self):
# Default unconnected
assert self.hub.local_fn == "example_hub.hub.txt"
assert self.hub.remote_fn == "example_hub.hub.txt"
assert self.hub.url is None
# Connecting components should not change hub
self.CONNECT()
assert self.hub.local_fn == "example_hub.hub.txt"
assert self.hub.remote_fn == "example_hub.hub.txt"
assert self.hub.url is None
self.DISCONNECT()
# set local/remote dir and fns should follow
self.hub.local_dir = "/data/hubs"
self.hub.remote_dir = "/remote/hubs"
assert self.hub.local_fn == "/data/hubs/example_hub.hub.txt", self.hub.local_fn
assert self.hub.remote_fn == "/remote/hubs/example_hub.hub.txt", self.hub.remote_fn
# resetting them should not change
self.hub.local_dir = None
self.hub.remote_dir = None
assert self.hub.local_fn == "example_hub.hub.txt"
assert self.hub.remote_fn == "example_hub.hub.txt"
# changing local_fn or remote_fn should stick -- and should override
# any set local/remote dir
self.hub.local_fn = "dummy.txt"
self.hub.remote_fn = "remote.txt"
self.hub.local_dir = "no_dir"
self.hub.remote_dir = "remote_dir"
assert self.hub.local_fn == "dummy.txt"
assert self.hub.remote_fn == "remote.txt"
def test_genome_file_fns(self):
assert_raises(AttributeError, getattr, self.genomes_file, "url")
# When unconnected, filenames should be None
assert self.genomes_file.local_fn is None
assert self.genomes_file.remote_fn is None
# ...though you can set them manually
self.genomes_file.local_fn = "local.genomes"
assert self.genomes_file.local_fn == "local.genomes"
self.genomes_file.local_fn = None
self.CONNECT()
assert self.genomes_file.local_fn == "example_hub.genomes.txt"
# when connected, overriding works
self.genomes_file.local_fn = "local.genomes"
assert self.genomes_file.local_fn == "local.genomes"
self.genomes_file.local_fn = None
# disconnecting brings it back to None
self.DISCONNECT()
assert self.genomes_file.local_fn is None
# set the hub's local_dir; genomes_file should follow.
self.CONNECT()
self.hub.local_dir = "local/"
assert self.genomes_file.local_fn == "local/example_hub.genomes.txt"
# what happens if the hub's local FN is changed?
self.hub.local_fn = "localhub/hub.txt"
assert self.genomes_file.local_fn == "localhub/example_hub.genomes.txt"
def test_genome_fns(self):
# should be easy -- filenames should raise attribute errors
assert_raises(AttributeError, getattr, self.genome, "local_fn")
assert_raises(AttributeError, getattr, self.genome, "remote_fn")
assert_raises(AttributeError, getattr, self.genome, "url")
def test_trackdb_fns(self):
assert_raises(AttributeError, getattr, self.trackdb, "url")
# when unconnected, no defaults
assert self.trackdb.local_fn is None
assert self.trackdb.remote_fn is None
self.CONNECT()
assert self.trackdb.local_fn == "dm3/trackDb.txt"
assert self.trackdb.remote_fn == "dm3/trackDb.txt"
# setting the local dir on the hub trickles down
self.hub.local_dir = "localdir"
assert self.trackdb.local_fn == "localdir/dm3/trackDb.txt"
# setting local_fn overrides
self.trackdb.local_fn = "mytrackdb.txt"
assert self.trackdb.local_fn == "mytrackdb.txt", self.trackdb.local_fn
# ...and back to None to reset
self.trackdb.local_fn = None
assert self.trackdb.local_fn == "localdir/dm3/trackDb.txt"
# genomes_file fn overrides
self.genomes_file.local_fn = "anotherdir/genomes.txt"
assert self.trackdb.local_fn == "anotherdir/dm3/trackDb.txt"
# reset parent hub and genomes file to get back to the default
self.genomes_file.local_fn = None
self.hub.local_dir = None
assert self.trackdb.local_fn == "dm3/trackDb.txt"
def test_track_fns(self):
for track in self.tracks:
assert track.local_fn is None
assert track.remote_fn is None
assert track.url is None
self.CONNECT()
# local fns should still be None
for track in self.tracks:
assert track.local_fn is None
# remote_fn is relative to the hub's remote_fn
assert self.tracks[0].remote_fn == "dm3/track1.bam"
assert self.tracks[1].remote_fn == "dm3/track2.bigWig"
self.hub.remote_fn = "/var/www/hubs/hub.txt"
self.hub.url = "http://example.com/hubs/hub.txt"
# URL is relative to the trackDb
assert self.tracks[0].url == "track1.bam"
def test_track_creation(self):
track = Track(name="track0", tracktype="bam", local_fn="t0.bam")
assert track.local_fn == "t0.bam"
class TestUpload(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bigBed',
source=os.path.join(d, 'random-hg38-0.bigBed')
),
Track(
name='track2',
tracktype='bigWig',
source=os.path.join(d, 'sine-hg38-0.bedgraph.bw'),
),
Track(
name='track3',
tracktype='bigWig',
source=os.path.join(d, 'sine-hg38-1.bedgraph.bw'),
filename='3.bw',
)
]
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def test_staging(self):
staging_dir, linknames = upload.stage_hub(self.hub)
assert open(os.path.join(staging_dir, 'example_hub.genomes.txt')).read() == dedent(
"""\
genome dm3
trackDb dm3/trackDb.txt
""")
assert open(os.path.join(staging_dir, 'example_hub.hub.txt')).read() == dedent(
"""\
hub hub
shortLabel example hub
longLabel an example hub for testing
genomesFile example_hub.genomes.txt
email [email protected]""")
#@unittest.skipUnless(os.path.exists('data/track1.bam'), 'No test data')
def test_upload(self):
d = tempfile.mkdtemp()
print(d)
upload.upload_hub(
hub=self.hub,
remote_dir=d,
user=None,
host=None,
)
def test_render(self):
trackdb = str(self.trackdb)
# make sure some of the trackdb rendered correctly
assert 'track track1' in trackdb
assert 'bigDataUrl track1.bigBed' in trackdb
assert 'bigDataUrl ../3.bw' in trackdb
class TestComponents(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(name='track1', tracktype='bam'),
Track(name='track2', tracktype='bigWig'),
]
def CONNECT(self):
self.hub.add_genomes_file(self.genomes_file)
self.genomes_file.add_genome(self.genome)
self.genome.add_trackdb(self.trackdb)
self.trackdb.add_tracks(self.tracks)
def DISCONNECT(self):
self.setup()
def test_self_connection(self):
"""
meta test: make sure the test class's connect/disconnect is working
"""
assert self.hub.genomes_file is None
self.CONNECT()
assert self.hub.genomes_file is self.genomes_file
self.DISCONNECT()
assert self.hub.genomes_file is None
# Filenames ---------------------------------------------------------------
def test_hub_fns(self):
# Default unconnected
assert self.hub.local_fn == 'example_hub.hub.txt'
assert self.hub.remote_fn == 'example_hub.hub.txt'
assert self.hub.url is None
# Connecting components should not change hub
self.CONNECT()
assert self.hub.local_fn == 'example_hub.hub.txt'
assert self.hub.remote_fn == 'example_hub.hub.txt'
assert self.hub.url is None
self.DISCONNECT()
# set local/remote dir and fns should follow
self.hub.local_dir = '/data/hubs'
self.hub.remote_dir = '/remote/hubs'
assert self.hub.local_fn == '/data/hubs/example_hub.hub.txt', \
self.hub.local_fn
assert self.hub.remote_fn == '/remote/hubs/example_hub.hub.txt', \
self.hub.remote_fn
# resetting them should not change
self.hub.local_dir = None
self.hub.remote_dir = None
assert self.hub.local_fn == 'example_hub.hub.txt'
assert self.hub.remote_fn == 'example_hub.hub.txt'
# changing local_fn or remote_fn should stick -- and should override
# any set local/remote dir
self.hub.local_fn = 'dummy.txt'
self.hub.remote_fn = 'remote.txt'
self.hub.local_dir = 'no_dir'
self.hub.remote_dir = 'remote_dir'
assert self.hub.local_fn == 'dummy.txt'
assert self.hub.remote_fn == 'remote.txt'
def test_genome_file_fns(self):
assert_raises(AttributeError, getattr, self.genomes_file, 'url')
# When unconnected, filenames should be None
assert self.genomes_file.local_fn is None
assert self.genomes_file.remote_fn is None
#...though you can set them manually
self.genomes_file.local_fn = 'local.genomes'
assert self.genomes_file.local_fn == 'local.genomes'
self.genomes_file.local_fn = None
self.CONNECT()
assert self.genomes_file.local_fn == 'example_hub.genomes.txt'
# when connected, overriding works
self.genomes_file.local_fn = 'local.genomes'
assert self.genomes_file.local_fn == 'local.genomes'
self.genomes_file.local_fn = None
# disconnecting brings it back to None
self.DISCONNECT()
assert self.genomes_file.local_fn is None
# set the hub's local_dir; genomes_file should follow.
self.CONNECT()
self.hub.local_dir = 'local/'
assert self.genomes_file.local_fn == 'local/example_hub.genomes.txt'
# what happens if the hub's local FN is changed?
self.hub.local_fn = 'localhub/hub.txt'
assert self.genomes_file.local_fn == 'localhub/example_hub.genomes.txt'
def test_genome_fns(self):
# should be easy -- filenames should raise attribute errors
assert_raises(AttributeError, getattr, self.genome, 'local_fn')
assert_raises(AttributeError, getattr, self.genome, 'remote_fn')
assert_raises(AttributeError, getattr, self.genome, 'url')
def test_trackdb_fns(self):
assert_raises(AttributeError, getattr, self.trackdb, 'url')
# when unconnected, no defaults
assert self.trackdb.local_fn is None
assert self.trackdb.remote_fn is None
self.CONNECT()
assert self.trackdb.local_fn == 'dm3/trackDb.txt'
assert self.trackdb.remote_fn == 'dm3/trackDb.txt'
# setting the local dir on the hub trickles down
self.hub.local_dir = 'localdir'
assert self.trackdb.local_fn == 'localdir/dm3/trackDb.txt'
# setting local_fn overrides
self.trackdb.local_fn = 'mytrackdb.txt'
assert self.trackdb.local_fn == 'mytrackdb.txt', self.trackdb.local_fn
# ...and back to None to reset
self.trackdb.local_fn = None
assert self.trackdb.local_fn == 'localdir/dm3/trackDb.txt'
# genomes_file fn overrides
self.genomes_file.local_fn = 'anotherdir/genomes.txt'
assert self.trackdb.local_fn == 'anotherdir/dm3/trackDb.txt'
# reset parent hub and genomes file to get back to the default
self.genomes_file.local_fn = None
self.hub.local_dir = None
assert self.trackdb.local_fn == 'dm3/trackDb.txt'
def test_track_fns(self):
for track in self.tracks:
assert track.local_fn is None
assert track.remote_fn is None
assert track.url is None
self.CONNECT()
# local fns should still be None
for track in self.tracks:
assert track.local_fn is None
assert self.tracks[0].remote_fn == 'dm3/track1.bam'
assert self.tracks[1].remote_fn == 'dm3/track2.bigWig'
self.hub.remote_fn = '/var/www/hubs/hub.txt'
self.hub.url = 'http://example.com/hubs/hub.txt'
print self.tracks[0].remote_fn
print self.hub.remote_fn
assert self.tracks[0].url == 'http://example.com/hubs/dm3/track1.bam'
def test_track_creation(self):
track = Track(name='track0', tracktype='bam', local_fn='t0.bam')
assert track.local_fn == 't0.bam'
assert args.composite_track_name is not None, "please provide the composite track name"
assert args.email is not None, "please provide your email"
assert args.input_dir is not None, "please provide the path to the bigwig and bigbed files on your local computer"
from trackhub import Hub, GenomesFile, Genome, TrackDb
hub = Hub(
hub='%s' % args.hub_name,
short_label='%s' % args.hub_name,
long_label='%s ChIP-seq hub' % args.hub_name,
email='%s' % args.email)
genomes_file = GenomesFile()
genome = Genome('hg19')
trackdb = TrackDb()
# Bottom-up
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
# make a composite track
from trackhub import CompositeTrack
composite = CompositeTrack(
name="%s" % args.composite_track_name,
short_label="%s" % args.composite_track_name,
long_label=" %s ChIP-seq" % args.composite_track_name,
tracktype="bigWig")
def files2viz(files_to_visualize):
if DEBUG:
print "Visualizing"
print files_to_visualize
from trackhub import Hub, GenomesFile, Genome, TrackDb, Track
from trackhub.upload import upload_hub
HUBHOST = 'http://cherry-vm45.stanford.edu'
HUBDIR = 'trackhubs'
USER = '******'
URLBASE = os.path.join(HUBHOST, HUBDIR)
EDWBASE = 'http://encodedcc.sdsc.edu/warehouse'
GENOME = 'hg19'
hub = Hub(
hub='Selected_ENCODE_Tracks',
short_label='Selected_ENCODE_Tracks_short',
long_label='Selected_ENCODE_Tracks_long',
email='*****@*****.**')
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
for accession in files_to_visualize:
file_obj = get_ENCODE(accession)
if DEBUG:
print file_obj
if file_obj['file_format'] == 'bigWig':
track = Track(
name=accession,
url=os.path.join(EDWBASE, str(file_obj['download_path'])),
tracktype='bigWig',
short_label=accession,
long_label=accession,
color='128,0,0',
visibility='full')
trackdb.add_tracks([track])
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results=hub.render()
if DEBUG:
print hub
print '...'
print genomes_file
print '...'
print genome
print '...'
print trackdb
#upload_hub(hub=hub, host=HUBHOST, user=USER) #doesn't seem to work
import subprocess
subprocess.call("cd .. && rsync -r trackhub [email protected]:/www/html/trackhubs", shell=True)
import webbrowser
hubfile = str(hub.hub) + '.hub.txt'
UCSC_url = 'http://genome.ucsc.edu/cgi-bin/hgTracks?udcTimeout=1&db=hg19' + \
'&hubUrl=' + os.path.join(HUBHOST,HUBDIR,'trackhub',hubfile) # + \
#'&hsS_doLoadUrl=submit' + '&hgS_loadUrlName=' + os.path.join(HUBHOST,HUBDIR,'trackhub','session.txt')
print UCSC_url
webbrowser.open(UCSC_url)
def ENCSR2viz(experiments_to_visualize):
if DEBUG:
print "Visualizing"
print experiments_to_visualize
from trackhub import Hub, GenomesFile, Genome, TrackDb, Track
from trackhub.upload import upload_hub
HUBHOST = 'http://cherry-vm45.stanford.edu'
HUBDIR = 'jseth/trackhubs'
USER = '******'
URLBASE = os.path.join(HUBHOST, HUBDIR)
EDWBASE = 'http://encodedcc.sdsc.edu/warehouse'
GENOME = 'hg19'
hub = Hub(
hub='ENCODE',
short_label='ENCODE',
long_label='ENCODE',
email='*****@*****.**')
genomes_file = GenomesFile()
genome = Genome(GENOME)
trackdb = TrackDb()
for accession in experiments_to_visualize:
experiment_obj = get_ENCODE(accession)
if DEBUG:
print experiment_obj
for file_id in experiment_obj['files']:
file_obj = get_ENCODE(file_id)
if file_obj['file_format'] in ['bigWig', 'bigBed', 'broadPeak', 'narrowPeak']:
if file_obj['file_format'] in ['bigWig']:
track_type = 'bigWig'
elif file_obj['file_format'] in ['bigBed', 'broadPeak', 'narrowPeak']:
track_type = 'bigBed'
track = Track(
name=str(file_obj['accession']),
url=os.path.join(EDWBASE, str(file_obj['download_path'])),
tracktype=track_type,
long_label=str(file_obj['accession']),
short_label=str(file_obj['output_type']),
color='128,0,0',
visibility='dense',
metadata='cell_type=primary')
print file_obj['accession']
trackdb.add_tracks([track])
genome.add_trackdb(trackdb)
genomes_file.add_genome(genome)
hub.add_genomes_file(genomes_file)
results=hub.render()
if DEBUG:
print hub
print '...'
print genomes_file
print '...'
print genome
print '...'
print trackdb
#upload_hub(hub=hub, host=HUBHOST, user=USER) #doesn't seem to work
import subprocess
subprocess.call("cd .. && rsync -r trackhub [email protected]:/www/html/jseth/trackhubs", shell=True)
import webbrowser
hubfile = str(hub.hub) + '.hub.txt'
UCSC_url = 'http://genome.ucsc.edu/cgi-bin/hgTracks?udcTimeout=1&db=hg19' + \
'&hubUrl=' + os.path.join(HUBHOST,HUBDIR,'trackhub',hubfile) # + \
#'&hsS_doLoadUrl=submit&hgS_loadUrlName=' + os.path.join(HUBHOST,HUBDIR,'trackhub','session.txt')
print UCSC_url
webbrowser.open(UCSC_url)